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/*
* The MIT License
*
* Wavefront Alignment Algorithms
* Copyright (c) 2017 by Santiago Marco-Sola <santiagomsola@gmail.com>
*
* This file is part of Wavefront Alignment Algorithms.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* PROJECT: Wavefront Alignment Algorithms
* AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
* DESCRIPTION: Score matrix for alignment using dynamic programming
*/
#ifndef SCORE_MATRIX_H_
#define SCORE_MATRIX_H_
#include "system/mm_allocator.h"
#include "alignment/cigar.h"
/*
* Constants
*/
#define SCORE_MAX (10000000)
/*
* Score Matrix
*/
typedef struct {
// Score Columns
int** columns;
int num_rows;
int num_columns;
// MM
mm_allocator_t* mm_allocator;
} score_matrix_t;
/*
* Setup
*/
void score_matrix_allocate(
score_matrix_t* const score_matrix,
const int num_rows,
const int num_columns,
mm_allocator_t* const mm_allocator);
void score_matrix_free(
score_matrix_t* const score_matrix);
/*
* Display
*/
void score_matrix_print(
FILE* const stream,
const score_matrix_t* const score_matrix,
const char* const pattern,
const char* const text);
#endif /* SCORE_MATRIX_H_ */
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